Elbow Plot for Clustering
Heatmap
Cluster Enrichments
Ectoderm Cluster
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
GO_Biological_Process_2018
KEGG_2019
Neuroectoderm Cluster
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
GO_Biological_Process_2018
KEGG_2019
Mesoderm Cluster
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
GO_Biological_Process_2018
KEGG_2019
Overlap between targets downregulated in WT vs. LOF and all clusters
Venn Diagram
Upset Plot
Resampling
Mesoderm
n
## [1] 50000
sum(res > 739)/n
## [1] 0
Neuroectoderm
n
## [1] 50000
sum(res > 292)/n
## [1] 0
Ectoderm
n
## [1] 50000
sum(res > 161)/n
## [1] 1
Overlap Enrichments
Downregulated & Neuroectoderm Overlap
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Downregulated & Mesoderm Overlap
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Mesoderm only
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Neuroectoderm only
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Downregulated only
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Overlap between targets UPREGULATED in WT vs. LOF and all clusters
Venn Diagram
Upset Plot
Resampling
Mesoderm
n
## [1] 50000
sum(res > 223)/n
## [1] 1
Neuroectoderm
n
## [1] 50000
sum(res > 109)/n
## [1] 0.99942
Ectoderm
n
## [1] 50000
sum(res > 629)/n
## [1] 0
Overlap Enrichments
Upregulated & Ectoderm Overlap
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Ectoderm only
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Upregulated only
## Uploading data to Enrichr... Done.
## Querying KEGG_2019... Done.
## Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.
Combined Upset Plot
Other Venn Diagrams
Session Info
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] png_0.1-7 UpSetR_1.4.0
## [3] enrichR_3.0 VennDiagram_1.6.20
## [5] futile.logger_1.4.3 org.Dm.eg.db_3.13.0
## [7] msigdbr_7.4.1 cowplot_1.1.1
## [9] ggpubr_0.4.0 data.table_1.14.0
## [11] DT_0.19 forcats_0.5.1
## [13] dplyr_1.0.7 purrr_0.3.4
## [15] readr_2.0.1 tidyr_1.1.3
## [17] tibble_3.1.4 tidyverse_1.3.1
## [19] factoextra_1.0.7 ggplot2_3.3.5
## [21] cluster_2.1.2 stringr_1.4.0
## [23] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.60.0
## [25] rtracklayer_1.52.1 Biostrings_2.60.2
## [27] XVector_0.32.0 pheatmap_1.0.12
## [29] geneplotter_1.70.0 annotate_1.70.0
## [31] XML_3.99-0.7 reshape_0.8.8
## [33] lattice_0.20-44 gridExtra_2.3
## [35] RColorBrewer_1.1-2 GenomicFeatures_1.44.2
## [37] AnnotationDbi_1.54.1 knitr_1.33
## [39] DESeq2_1.32.0 SummarizedExperiment_1.22.0
## [41] Biobase_2.52.0 MatrixGenerics_1.4.3
## [43] matrixStats_0.60.1 GenomicRanges_1.44.0
## [45] GenomeInfoDb_1.28.4 IRanges_2.26.0
## [47] S4Vectors_0.30.0 BiocGenerics_0.38.0
##
## loaded via a namespace (and not attached):
## [1] readxl_1.3.1 backports_1.2.1 BiocFileCache_2.0.0
## [4] plyr_1.8.6 splines_4.1.1 crosstalk_1.1.1
## [7] BiocParallel_1.26.2 digest_0.6.27 htmltools_0.5.2
## [10] fansi_0.5.0 magrittr_2.0.1 memoise_2.0.0
## [13] tzdb_0.1.2 openxlsx_4.2.4 modelr_0.1.8
## [16] prettyunits_1.1.1 colorspace_2.0-2 blob_1.2.2
## [19] rvest_1.0.1 rappdirs_0.3.3 ggrepel_0.9.1
## [22] haven_2.4.3 xfun_0.25 crayon_1.4.1
## [25] RCurl_1.98-1.4 jsonlite_1.7.2 genefilter_1.74.0
## [28] survival_3.2-11 glue_1.4.2 gtable_0.3.0
## [31] zlibbioc_1.38.0 DelayedArray_0.18.0 car_3.0-11
## [34] abind_1.4-5 scales_1.1.1 futile.options_1.0.1
## [37] DBI_1.1.1 rstatix_0.7.0 Rcpp_1.0.7
## [40] xtable_1.8-4 progress_1.2.2 foreign_0.8-81
## [43] bit_4.0.4 htmlwidgets_1.5.4 httr_1.4.2
## [46] ellipsis_0.3.2 farver_2.1.0 pkgconfig_2.0.3
## [49] dbplyr_2.1.1 locfit_1.5-9.4 utf8_1.2.2
## [52] labeling_0.4.2 tidyselect_1.1.1 rlang_0.4.11
## [55] munsell_0.5.0 cellranger_1.1.0 tools_4.1.1
## [58] cachem_1.0.6 cli_3.0.1 generics_0.1.0
## [61] RSQLite_2.2.8 broom_0.7.9 evaluate_0.14
## [64] fastmap_1.1.0 yaml_2.2.1 babelgene_21.4
## [67] bit64_4.0.5 fs_1.5.0 zip_2.2.0
## [70] KEGGREST_1.32.0 formatR_1.11 xml2_1.3.2
## [73] biomaRt_2.48.3 compiler_4.1.1 rstudioapi_0.13
## [76] filelock_1.0.2 curl_4.3.2 ggsignif_0.6.2
## [79] reprex_2.0.1 stringi_1.7.4 highr_0.9
## [82] Matrix_1.3-4 vctrs_0.3.8 pillar_1.6.2
## [85] lifecycle_1.0.0 jquerylib_0.1.4 bitops_1.0-7
## [88] R6_2.5.1 BiocIO_1.2.0 rio_0.5.27
## [91] lambda.r_1.2.4 assertthat_0.2.1 rprojroot_2.0.2
## [94] rjson_0.2.20 withr_2.4.2 GenomicAlignments_1.28.0
## [97] Rsamtools_2.8.0 GenomeInfoDbData_1.2.6 hms_1.1.0
## [100] rmarkdown_2.10 carData_3.0-4 lubridate_1.7.10
## [103] restfulr_0.0.13